Merge pull request #19 from trendelkampschroer/devel

Hyperlinks for objects returned by msmapi in docu
[Cython] Enforce usage of cython for sdist archive creation and when on git, since
we do not want to distribute generated code in repository.
[ci] only make docs on regular commits, not pull requests
Merge pull request #20 from marscher/cythonize_on_sdist_or_git

[Cython] Enforce usage of cython for sdist archive creation and when on git
[msm-api] fixed links to classes. Use PEP8 formatting.
[sphinx] import pyemma from a relative path. Inserting in sys.path sometimes import from installed package
fix returns: -> returns
move submodule ipython to new location
[hmm] handle java exception and reraise as RuntimeError
[msm/analysis] Tolerance for assessment functions is now tol=1e-12
[msm/analysis] Unit test contains large transition matrix example to capture too restrictive tol parameter in is_transition_matrix. Fixes #23